PlotPies: Plot comparison with other clustering

Description Usage Arguments Value See Also Examples

View source: R/3_buildMST.R

Description

Plot FlowSOM grid or tree, with pies indicating another clustering or manual gating result

Usage

1
2
3
4
5
6
PlotPies(fsom, cellTypes, view = "MST",
  colorPalette = grDevices::colorRampPalette(c("white", "#00007F", "blue",
  "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red")),
  backgroundValues = NULL, backgroundColor = function(n) {    
  grDevices::rainbow(n, alpha = 0.3) }, backgroundLim = NULL,
  backgroundBreaks = NULL, legend = TRUE, main = "")

Arguments

fsom

FlowSOM object, as generated by BuildMST

cellTypes

Array of factors indicating the celltypes

view

Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)

colorPalette

Colorpalette to be used for the markers

backgroundValues

Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering)

backgroundColor

Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors

backgroundLim

Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.

backgroundBreaks

Breaks to pass on to cut, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).

legend

Logicle, if T add a legend

main

Title of the plot

Value

Nothing is returned. A plot is drawn in which each node is represented by a pie chart indicating the percentage of cells present of each cell type. At the end, the layout is set to 1 figure again.

See Also

PlotStars,PlotMarker, PlotCenters,BuildMST

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
   # Read from file, build self-organizing map and minimal spanning tree
   fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")
   flowSOM_res <- FlowSOM(fileName, compensate=TRUE,transform=TRUE,
                            scale=TRUE,colsToUse=c(9,12,14:18),nClus=7)
   ff <- flowCore::read.FCS(fileName)
   ff_c <- flowCore::compensate(ff,flowCore::description(ff)$SPILL)
   flowCore::colnames(ff_c)[8:18] <- paste("Comp-",
                                     flowCore::colnames(ff_c)[8:18],
                                     sep="")
   
   # Get the manually gated labels using a gatingML file 
   gatingFile <- system.file("extdata","manualGating.xml", 
                             package="FlowSOM")
   gateIDs <- c( "B cells"=8,
                 "ab T cells"=10,
                 "yd T cells"=15,
                 "NK cells"=5,
                 "NKT cells"=6)
   cellTypes <- c("B cells","ab T cells","yd T cells",
                 "NK cells","NKT cells")
   gatingResult <- ProcessGatingML(ff_c, gatingFile, gateIDs, cellTypes)
       
   
   # Plot pies indicating the percentage of cell types present in the nodes
   PlotPies(flowSOM_res[[1]],gatingResult$manual)

FlowSOM documentation built on May 31, 2017, 11:26 a.m.

Search within the FlowSOM package
Search all R packages, documentation and source code